1. Mechanical Force and Biomolecules Lecture 2: Overview of biomolecular structure

3. Ribose vs. Deoxyribose
Throughout: images from online version of “Biochemistry” by Berg, Tymoczko, and Stryer

4. Sugar phosphate backbone

5. Nucleic acids: bases
DNA: A, G, T, C
RNA: A, G, U, C

6. Watson-Crick Basepairing joins 2 chains
Two chains with complementary sequences will basepair, and coil around each other to form a double helix

7. The double helix is anti-parallel and asymmetric

8. Double-helix is asymmetric (major and minor groove); each groove has unique pattern of H-bonding- permits bp-specific binding to grooves (e.g. by other N.A., protein)

9. Single-stranded nucleic acids can fold into complex structures
This is a Ribozyme- an RNA structure that can act as an enzyme, and catalyze reactions

10. Proteins

11. Amino acids are chiral
From Berg et al, Biochemistry (NCBI books website)

12. Peptide bonds link amine to carboxylate

13. Side chains Simple aliphatic: Glycine: R = Hydrogen
Alanine: R = methyl
Small, so not much h-phobic effect 2

14. Larger
Aliphatic;
Large h-phobic effect 6

15. Proline: also aliphatic, but not averse to H2O
Cyclization makes poly-proline chains very rigid 7

16. Tyr: reactive hydroxyl
Aromatic rings
Tyr: reactive hydroxyl
Trp and Tyr: strongly absorb UV light (commonly used to quantify protein concentration) 10

17. Hydrophilic due to hydroxyl group12

18. Cysteine
Sulfur can form covalent di-sulfide bonds; important for labelling! 13

19. Basic side chains: (+) charge, hydrophilic
pK = 6.5 (His), 12.0 (arg), 10.0 (Lys) 16

20. Acidic 20

21. Large variety in physical properties of amino acids leads to a large variety of protein structures. Typically, these are classified in a hierarchy of: Primary = a.a. sequence Secondary = local folded structures Tertiary = Globular arrangement of chain Quaternary = Association of multiple chains

22. Secondary structure: Alpha helix (typically right-handed)
Amine at position n H-bonds with CO at position n+4

23. Secondary: Beta sheet
Anti-parallel
Parallel

24. Tertiary structure: Arrangement of local motifs into compact, globular structure:

25. Quaternary structure: Arrangement of multiple chains into a multi-meric complex